Enterobacter kobei sp. nov., a new species of the family Enterobacteriaceae resembling Enterobacter cloacae

Genomic and biotechnological potential of a novel oil-degrading strain Enterobacter kobei DH7 isolated from petroleum-contaminated soil

In this study, a novel oil-degrading strain Enterobacter kobei DH7 was isolated from petroleum-contaminated soil samples from the industrial park in Taolin Town, Lianyungang, China. The whole genome of the strain was sequenced and analyzed to reveal its genomic potential. The oil degradation and growth conditions including nitrogen, and phosphorus sources, degradation cycle, biological dosing, pH, and oil concentration were optimized to exploit its commercial application. The genome of the DH7 strain contains 4,705,032 bp with GC content of 54.95% and 4653 genes. The genome analysis revealed that there are several metabolic pathways and enzyme-encoding genes related to oil degradation in the DH7 genome, such as the paa gene cluster which is involved in the phenylacetic acid degradation pathway, and complete degradation pathways for fatty acid and benzoate, genes related to chlorinated alkanes and olefins degradation pathway including adhP, frmA, and adhE, etc. The strain DH7 under the optimized conditions has demonstrated a maximum degradation efficiency of 84.6% after 14 days of treatment using synthetic oil, which comparatively displays a higher oil degradation efficiency than any Enterobacter species known to date. To the best of our knowledge, this study presents the first-ever genomic studies related to the oil degradation potential of any Enterobacter species. As Enterobacter kobei DH7 has demonstrated significant oil degradation potential, it is one of the good candidates for application in the bioremediation of oil-contaminated environments.

Bacterial Communities of the Internal Reproductive and Digestive Tracts of Virgin and Mated Tuta absoluta

Microorganisms can affect host reproduction, defense, and immunity through sexual or opportunistic transmission; however, there are few studies on insect reproductive organs and intestinal bacterial communities and their effects on mating. Tuta absoluta is a worldwide quarantine pest that seriously threatens the production of Solanaceae crops, and the microbial community within tomato leafminers remains unclear. In this study, 16s rRNA sequencing was used to analyze bacterial communities related to the reproductive organs and intestinal tracts of tomato leafminers (the sample accession numbers are from CNS0856533 to CNS0856577). Different bacterial communities were found in the reproductive organs and intestinal tracts of females and males. Community ecological analysis revealed three potential signs of bacterial sexual transmission: (1) Mating increased the similarity between male and female sex organs and intestinal communities. (2) The bacteria carried by mated individuals were found in unmated individuals of the opposite sex but not in unmated individuals of the same sex. (3) The bacteria carried by unmated individuals were lost after mating. In addition, the abundances of bacterial communities carried by eggs were significantly higher than those of adult worms. Our results confirm that mating leads to the transfer of bacterial communities in the reproductive organs and gut of tomato leafminers, and suggest that this community strongly influences the reproductive process.

Multidrug-resistant Enterobacter spp. in wastewater and surface water: Molecular characterization of β-lactam resistance and metal tolerance genes

Among the ESKAPE group pathogens, Enterobacter spp. is an opportunistic Gram-negative bacillus, widely dispersed in the environment, that causes infections. In the present study, samples of hospital wastewater, raw and treated urban wastewater, as well as surface receiving water, were collected to assess the occurrence of multidrug-resistant (MDR) Enterobacter spp. A molecular characterization of β-lactam antibiotic resistance and metal tolerance genes was performed. According to identification by MALDI-TOF MS, 14 isolates were obtained: 7 E. bugandensis, 5 E. kobei, and 2 E. cloacae. The isolates showed resistance mainly to β-lactam antibiotics, including those used to treat infections caused by MDR bacteria. Multiple antibiotic resistance index was calculated for all isolates. It allowed verify whether sampling points showed a high risk due to antibiotic resistant Enterobacter spp., as well as to determine if the isolates have been in environments with a frequent antibiotic use. Twelve isolates showed β-lactam antibiotic resistance gene, being the blaKPC widely detected. Regarding metal tolerance, 13 isolates showed at least two genes that encode metal tolerance mechanisms. Overall, metal tolerance mechanisms to silver, copper, mercury, arsenic and tellurium were found. New data on metal tolerance mechanisms dispersion and antibiotic-resistance characterization of the E. bugandensis and E. kobei species were here provided. The occurrence of MDR Enterobacter spp. in analyzed samples draws attention to an urgent need to put control measures into practice. It also evidences waterborne spread of clinically important antibiotic-resistant bacteria recognized as critical priority pathogens.

Co-occurrence of blaNDM-1, rmtC, and mcr-9 in multidrug-resistant Enterobacter kobei strain isolated from an infant with urinary tract infection

OBJECTIVES

The co-emergence of mcr and carbapenem resistance genes in Gram-negative bacteria is a serious problem. This study aims to clarify the genetic characteristic of one novel multidrug-resistant Enterobacter kobei EC1382 with mcr-9 causing urinary tract inflammation in an infant.

METHODS

Antimicrobial drug susceptibility testing was performed for this isolate using the broth microdilution method. Whole-genome sequencing was performed using the Illumina PacBio RS II platform and HiSeq platform, and the antimicrobial resistance genes, mobile elements, and plasmid replicon types were identified. Conjugation analysis was performed using Escherichia coli C600 as recipients.

RESULTS

Enterobacter kobei EC1382 was resistant to carbapenem, aminoglycoside, and cephalosporin. Twenty-five antimicrobial resistance genes were identified, including genes conferring resistance to carbapenem (blaNDM-1), colistin (mcr-9), and aminoglycosides (rmtC). The blaNDM-1 gene, accompanied by bleMBL and rmtC located downstream of an ISCR14 element, was detected in the IncFII(Yp) type plasmid pEC1382-2. Interestingly, although E. kobei EC1382 was susceptible to colistin, it had three identical mcr-9 genes (two in the chromosome and one in the IncHI2-type plasmid pEC1382-1). The backbone (∼12.2-kb genetic fragment) of these mcr-9 (flanked by IS903B and IS481-IS26) regions were conserved in this strain, and they were found to be present in various bacteria as three types, implying a silent distribution.

CONCLUSIONS

To the best of our knowledge, this is the first study to demonstrate the coexistence of blaNDM-1, rmtC, and mcr-9 in E. kobei. The silent prevalence of mcr-9 in bacteria may be a threat to public health.

Screening and isolation of acid-tolerant bacteria using a novel pH shift culture method

Acid-tolerant bacteria, which multiply under neutral pH and can survive under acidic pH conditions, have a potential role in various applications under acidic conditions. Despite higher biomass productivity, their isolation and utilisation are not sufficiently developed compared to those of acidophiles. It takes considerable effort to distinguish the acid-tolerant bacteria from the rest of the bacterial community using conventional screening methods. Thus, we developed a novel screening method for acid-tolerant bacteria, which involves shifting the pH between acidic and neutral conditions. With this method, the bacterium Enterobacter sp. AC06 was isolated. Based on comparisons with the results reported in previous studies, the strain can be classified as acid-tolerant bacteria. The decreases in the live cell concentrations were 3.87 and 6.16 log cycles after 3 h acid treatment under pH 3.0 and 2.5, respectively. These results suggest that it is possible to isolate acid-tolerant bacteria using the pH shift culture method. In summary, this is the first study on bacterial screening based on acid tolerance. Our novel method potentially contributes to the understanding and utilisation of acid-tolerant bacteria by enhancing screening efficiency. Furthermore, our novel concept shift culture is potentially valuable for screening previously uncultured bacteria tolerant to various selective stress conditions.

Effects of epiphytic and exogenous lactic acid bacteria on fermentation quality and microbial community compositions of paper mulberry silage

This study aimed to isolate, characterize, and identify lactic acid bacteria (LAB) strains from various sources and evaluate their effects on the nutritional quality, fermentation characteristics, and microbial compositions of paper mulberry (PM) after 60 days of ensiling. Forty-nine LAB strains were isolated from Phalaris arundinacea silage, pickle, and fresh PM leaves; three of these strains (Lactiplantibacillus plantarum, YC1; Levilactobacillus brevis, PC3; and Lactiplantibacillus plantarum, BP17) and one commercial inoculant Gaofuji (GFJ) were subsequently used. Compared with other treatments, PC3 and BP17 increased (P < 0.05) the LAB count and crude protein content and decreased (P < 0.05) the molds and coliform bacteria counts, pH, and ammonia-N content of PM silages. BP17 and PC3 increased the relative Lactiplantibacillus abundance and decreased that of Lelliottia and Cladosporium, improving PM silage quality. Therefore, PC3 and BP17 can improve the fermentation quality of PM silage and could be used as silage starter cultures.

Revisiting Species Identification within the Enterobacter cloacae Complex by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify pathogens, despite some limitations of the technique. The Enterobacter cloacae complex (ECC) taxonomy has recently been expanded, leading to uncertain identification of some species within the ECC when commercial MALDI-TOF MS is used. This technique is especially unsuited in the case of E. hormaechei, the main species responsible for infections and one of the most prone, within the ECC, to acquire antibiotic resistance. Hence, rapid and reliable identification at the species level could improve patient management. Here, we evaluated the performance of the Bruker Microflex MALDI-TOF MS instrument to identify ECC isolates using two databases and algorithms in comparison to the hsp60 gene sequencing reference method: the Bruker database included in the MALDI Biotyper software and an extensive online database coupled to an original Mass Spectrometric Identification (MSI) algorithm. Among a panel of 94 ECC isolates tested in triplicate, the online database coupled to MSI software allowed the highest rate of identification at the species level (92%) compared to the MALDI Biotyper database (25%), especially for the species E. hormaechei (97% versus 20%). We show that by creating a database of MALDI-TOF reference spectral profiles with a high number of representatives associated with the performant MSI software, we were able to substantially improve the identification of the E. cloacae complex members, with only 8% of isolates misidentified at the species level. This online database is available through a free online MSI application (https://msi.happy-dev.fr/). IMPORTANCE Creation of a database of MALDI-TOF reference spectral profiles with a high number of representatives associated with the performant MSI software enables substantial improvement in identification of E. cloacae complex members. Moreover, this online database is available through a free online MSI application (https://msi.happy-dev.fr/).

Identification of Non- Streptococcus mutans Bacteria from Predente Infant Saliva Grown on Mitis-Salivarius-Bacitracin Agar

Objective: Although mitis-salivarius-bacitracin (MSB) agar is a commonly used selective medium for detecting Streptococcus mutans in clinical studies, non-S. mutans microorganisms are cultivatable on MSB agar. Since few studies have identified non-S. mutans bacteria grown on MSB, this study aimed to identify and differentiate MSB-grown non-S. mutans bacteria from predente infants' oral cavity. Study design: The saliva from 51 predente infants were plated on MSB agars. Bacteria colonies were characterized based on their morphology under direct visualization and light microscopic observation. Colony PCR targeting S. mutans htrA locus and 16S rRNA DNA sequencing were used for further bacteria identification. Results: Overall, 80% of the predente infants had oral bacteria grown on the MSB agar. Nine bacteria were identified, including S. mutans, Staphylococcus epidermidis, Klebsiella quasi-pneumoniae, Klebsiella pneumoniae, Enterobacter kobei, Enterococcus faecalis, Staphylococcus hominis, Streptococcus anginosus and Phytobacter. The most frequently detected bacteria were S. epidermidis (41.5%), followed by E. kobei (24.4%), K. pneumoniae (17.1%) and S. mutans (9.8%.) Conclusions: Multiple non-S. mutans bacteria from infants' oral cavity could grow on MSB agar. Caution should be exercised in counting the colony forming units of S. mutans from oral samples on MSB agar to avoid overestimation by assuming that all colonies on the MSB agar are S. mutans. Using the colony morphological guide we summarized, these non-S. mutans bacteria could be distinguished from S. mutans. Our study provides a key reference to pediatric cariology clinical-epidemiological studies that commonly use MSB to identify/quantify S. mutans in infants and young children.

Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance

The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. First described in 1960, this group member has proven to be more complex as a result of the exponential evolution of phenotypic and genotypic methods. Today, 22 species belong to the Enterobacter genus. These species are described in the environment and have been reported as opportunistic pathogens in plants, animals, and humans. The pathogenicity/virulence of this bacterium remains rather unclear due to the limited amount of work performed to date in this field. In contrast, its resistance against antibacterial agents has been extensively studied. In the face of antibiotic treatment, it is able to manage different mechanisms of resistance via various local and global regulator genes and the modulation of the expression of different proteins, including enzymes (β-lactamases, etc.) or membrane transporters, such as porins and efflux pumps. During various hospital outbreaks, the Enterobacter aerogenes and E. cloacae complex exhibited a multidrug-resistant phenotype, which has stimulated questions about the role of cascade regulation in the emergence of these well-adapted clones.

Draft Genome Sequence of the Histamine-Producing Bacterium Enterobacter kobei Strain 42-12

Bacterially produced histamine in food can be a cause of food poisoning. The whole-genome sequence is described for one histamine-producing Enterobacter kobei 42-12 isolate from the edible portion of salted, dried fish.

Bacterially produced histamine in food can be a cause of food poisoning. The whole-genome sequence is described for one histamine-producing Enterobacter kobei 42-12 isolate from the edible portion of salted, dried fish.

Multidrug-Resistant Enterobacter cloacae Complex Emerging as a Global, Diversifying Threat

The Enterobacter cloacae complex (ECC) includes common nosocomial pathogens capable of producing a wide variety of infections. Broad-spectrum antibiotic resistance, including the recent emergence of resistance to last-resort carbapenems, has led to increased interest in this group of organisms and carbapenem-resistant E. cloacae complex (CREC) in particular. Molecular typing methods based on heat-shock protein sequence, pulsed-field gel electrophoresis, comparative genomic hybridization, and, most recently, multilocus sequence typing have led to the identification of over 1069 ECC sequence types in 18 phylogenetic clusters across the globe. Whole-genome sequencing and comparative genomics, moreover, have facilitated global analyses of clonal composition of ECC and specifically of CREC. Epidemiological and genomic studies have revealed diverse multidrug-resistant ECC clones including several potential epidemic lineages. Together with intrinsic β-lactam resistance, members of the ECC exhibit a unique ability to acquire genes encoding resistance to multiple classes of antibiotics, including a variety of carbapenemase genes. In this review, we address recent advances in the molecular epidemiology of multidrug-resistant E. cloacae complex, focusing on the global expansion of CREC.

Infections Caused by Antimicrobial Drug-Resistant Saprophytic Gram-Negative Bacteria in the Environment

Background

Drug-resistance genes found in human bacterial pathogens are increasingly recognized in saprophytic Gram-negative bacteria (GNB) from environmental sources. The clinical implication of such environmental GNBs is unknown.

Objectives

We conducted a systematic review to determine how often such saprophytic GNBs cause human infections.

Methods

We queried PubMed for articles published in English, Spanish, and French between January 2006 and July 2014 for 20 common environmental saprophytic GNB species, using search terms “infections,” “human infections,” “hospital infection.” We analyzed 251 of 1,275 non-duplicate publications that satisfied our selection criteria. Saprophytes implicated in blood stream infection (BSI), urinary tract infection (UTI), skin and soft tissue infection (SSTI), post-surgical infection (PSI), osteomyelitis (Osteo), and pneumonia (PNA) were quantitatively assessed.

Results

Thirteen of the 20 queried GNB saprophytic species were implicated in 674 distinct infection episodes from 45 countries. The most common species included Enterobacter aerogenes, Pantoea agglomerans, and Pseudomonas putida. Of these infections, 443 (66%) had BSI, 48 (7%) had SSTI, 36 (5%) had UTI, 28 (4%) had PSI, 21 (3%) had PNA, 16 (3%) had Osteo, and 82 (12%) had other infections. Nearly all infections occurred in subjects with comorbidities. Resistant strains harbored extended-spectrum beta-lactamase (ESBL), carbapenemase, and metallo-β-lactamase genes recognized in human pathogens.

Conclusion

These observations show that saprophytic GNB organisms that harbor recognized drug-resistance genes cause a wide spectrum of infections, especially as opportunistic pathogens. Such GNB saprophytes may become increasingly more common in healthcare settings, as has already been observed with other environmental GNBs such as Acinetobacter baumannii and Pseudomonas aeruginosa.

Enterobacter cloacae complex: clinical impact and emerging antibiotic resistance

Species of the Enterobacter cloacae complex are widely encountered in nature, but they can act as pathogens. The biochemical and molecular studies on E. cloacae have shown genomic heterogeneity, comprising six species: Enterobacter cloacae, Enterobacter asburiae, Enterobacter hormaechei, Enterobacter kobei, Enterobacter ludwigii and Enterobacter nimipressuralis, E. cloacae and E. hormaechei are the most frequently isolated in human clinical specimens. Phenotypic identification of all species belonging to this taxon is usually difficult and not always reliable; therefore, molecular methods are often used. Although the E. cloacae complex strains are among the most common Enterobacter spp. causing nosocomial bloodstream infections in the last decade, little is known about their virulence-associated properties. By contrast, much has been published on the antibiotic-resistance features of these microorganisms. In fact, they are capable of overproducing AmpC β-lactamases by derepression of a chromosomal gene or by the acquisition of a transferable ampC gene on plasmids conferring the antibiotic resistance. Many other resistance determinants that are able to render ineffective almost all antibiotic families have been recently acquired. Most studies on antimicrobial susceptibility are focused on E. cloacae, E. hormaechei and E. asburiae; these studies reported small variations between the species, and the only significant differences had no discriminating features.

Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter

The taxonomy of Enterobacter has a complicated history, with several species transferred to and from this genus. Classification of strains is difficult owing to its polyphyletic nature, based on 16S rRNA gene sequences. It has been previously acknowledged that Enterobacter contains species which should be transferred to other genera. In an attempt to resolve the taxonomy of Enterobacter, MLSA based on partial sequencing of protein-encoding genes (gyrB, rpoB, infB and atpD) was performed on the type strains and reference strains of Enterobacter, Cronobacter and Serratia species, as well as members of the closely related genera Citrobacter, Klebsiella, Kluyvera, Leclercia, Mangrovibacter, Raoultella and Yokenella. Phylogenetic analyses of the concatenated nucleotide sequences revealed that Enterobacter can be divided into five strongly supported MLSA groups, suggesting that the species should be reclassified into five different genera. Further support for this was provided by a concatenated amino acid tree, phenotypic characteristics and fatty acid profiles, enabling differentiation of the MLSA groups. Three novel genera are proposed: Lelliottia gen. nov., Pluralibacter gen. nov. and Kosakonia gen. nov. and the following new combinations: Lelliottia nimipressuralis comb. nov., Lelliottia amnigena comb. nov., Pluralibacter gergoviae comb. nov., Pluralibacter pyrinus comb. nov., Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov., Kosakonia arachidis comb. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov. Additionally, the novel epithet Cronobacter zurichensis nom. nov. is proposed for the reclassification of Enterobacter turicensis into the genus Cronobacter, as Cronobacter turicensis (Iversen et al., 2008) is already in use.

Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov

Enterobacter massiliensis strain JC163(T) sp. nov. is the type strain of E. massiliensis sp. nov., a new species within the genus Enterobacter. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. E. massiliensis is an aerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,922,247 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 55.1% and contains 4,644 protein-coding and 80 RNA genes, including 5 rRNA genes.

Genomic diversity within the Enterobacter cloacae complex

Background

Isolates of the Enterobacter cloacae complex have been increasingly isolated as nosocomial pathogens, but phenotypic identification of the E. cloacae complex is unreliable and irreproducible. Identification of species based on currently available genotyping tools is already superior to phenotypic identification, but the taxonomy of isolates belonging to this complex is cumbersome.

Methodology/Principal Findings

This study shows that multilocus sequence analysis and comparative genomic hybridization based on a mixed genome array is a powerful method for studying species assignment within the E. cloacae complex. The E. cloacae complex is shown to be evolutionarily divided into two clades that are genetically distinct from each other. The younger first clade is genetically more homogenous, contains the Enterobacter hormaechei species and is the most frequently cultured Enterobacter species in hospitals. The second and older clade consists of several (sub)species that are genetically more heterogonous. Genetic markers were identified that could discriminate between the two clades and cluster 1.

Conclusions/Significance

Based on genomic differences it is concluded that some previously defined (clonal and heterogenic) (sub)species of the E. cloacae complex have to be redefined because of disagreements with known or proposed nomenclature. However, further improved identification of the redefined species will be possible based on novel markers presented here.

A toxaphene-degrading bacterium related to Enterobacter cloacae, strain D1 isolated from aged contaminated soil in Nicaragua

Enterobacter sp. strain D1 is a facultative anaerobic, Gram-negative heterotrophic bacterium isolated from toxaphene-contaminated soil. This organism was identified and characterized through phylogenetic and taxonomic studies. Based on 16S rDNA analysis, the strain D1 was clustered closely with the species Enterobacter cloacae subsp. dissolvens (LMG 2683) and E. cloacae (ATCC 13047T). Strain D1 resembled these E. cloacae strains with respect to various biochemical and nutritional characteristics, but also exhibited differences. Moreover, strain D1 is able to grow and survive with toxaphene supplied in the medium in the range 3-96 mg/L. Amongst the chemical components of toxaphene, octachlorocamphenes, nonachlorobornanes and decachlorobornanes were seen to be rapidly metabolized, although levels of hexachlorocamphenes and heptachlorobornanes were found to be slowly degraded, and subsequently accumulated during the last stage of the cultivation.

Nosocomial urosepsis caused by Enterobacter kobei with aberrant phenotype

Enterobacter kobei is the species of the Enterobacter cloacae complex, which is phenotypically most closely related to the species E. cloacae. This is the first report of infection caused by a new biotype of E. kobei. A patient with a history of urinary bladder operation developed a urosepsis with an Enterobacter isolate displaying the E. cloacae phenotype. The isolate was classified to the species E. kobei by sequence analysis of the 16S-rDNA, 4 protein-coding genes and enterobacterial repetitive intergenic consensus (ERIC)-cluster analysis. E. kobei was originally described to be Voges-Proskauer (VP) negative. However, the isolates of the present case were VP-positive. After analyzing 120 biochemical tests included in the API20E and the Biotype 100 systems, 4 biochemical tests were identified potentially differentiating this new biotype from E. cloacae.

Reassignment of enterobacter dissolvens to Enterobacter cloacae as E. cloacae subspecies dissolvens comb. nov. and emended description of Enterobacter asburiae and Enterobacter kobei

The taxonomic position of Enterobacter dissolvens was re-evaluated based on the analysis of the type strain ATCC 23373T and three clinical isolates. The strains were assigned to the genetic cluster of the species by phylogenetic sequence analysis in the frame of a recent population genetic study. The relatedness of E. dissolves to the other species of the E. cloacae complex was analyzed by DNA-DNA hybridization studies based on melting profiles in microplates. The genetic cluster of E. dissolvens fell into the same DNA-relatedness group like E. cloacae with mean deltaTm-values of 3.9 degrees C confirming the hybridization results of three former studies. Phenotypic analysis of the E. cloacae and E. dissolvens strains, respectively, based on 115 biochemical reactions yielded the esculin test as the only one differentiating between them by being positive for E. dissolvens and negative for E. cloacae strains. The name E. cloacae subsp. dissolvens comb. nov. is proposed for the group of organisms formerly referred to as E. dissolvens, and the name E. cloacae subsp. cloacae comb. nov. for the group of organisms formerly referred to as E. cloacae. The species descriptions of Enterobacter kobei and Enterobacter asburiae were emended based on the data collected on 17 and 15 strains, respectively. The strains were assigned to the respective species by a combination of phylogenetic sequence analyzes and DNA-DNA hybridizations. Phenotypic analyzes of 115 reactions gave detailed species profiles with new differentiating phenotypic properties.

Description of Enterobacter ludwigii sp. nov., a novel Enterobacter species of clinical relevance

A new species, Enterobacter ludwigii, is presented on the basis of the characteristics of 16 strains, which were isolated from clinical specimens. These bacteria form a distinct genetic cluster in phylogenetic analyses of the population structure of the Enterobacter cloacae complex. As determined by DNA-DNA cross-hybridization experiments in microplates, this genetic cluster can be delineated from the other species of the E. cloacae complex with deltaTm values equal to or above 5 degrees C with Enterobacter hormaechei being the closest relative. The bacteria are gram-negative, fermentative, motile rods with the general characteristics of the genus Enterobacter and the E. cloacae complex in particular. E. ludwigii can be differentiated from the other Enterobacter species by its growth on myo-inositol and 3-0-methyl-D-glucopyranose. The type strain is EN-119 (= DSM 16688T = CIP 108491T).

Population genetics of the nomenspecies Enterobacter cloacae

The genetic heterogeneity of the nomenspecies Enterobacter cloacae is well known. Enterobacter asburiae, Enterobacter cancerogenus, Enterobacter dissolvens, Enterobacter hormaechei, Enterobacter kobei, and Enterobacter nimipressuralis are closely related to it and are subsumed in the so-called E. cloacae complex. DNA-DNA hybridization studies performed previously identified at least five DNA-relatedness groups of this complex. In order to analyze the genetic structure and the phylogenetic relationships between the clusters of the nomenspecies E. cloacae, 206 strains collected from 22 hospitals, a veterinarian, and an agricultural center in 11 countries plus all 13 type strains of the genus and reference strain CDC 1347-71(R) were examined with a combination of sequence and PCR-restriction fragment length polymorphism (PCR-RFLP) analyses of the three housekeeping genes hsp60, rpoB, and hemB as well as ampC, the gene of a class C beta-lactamase. Based on the neighbor-joining tree of the hsp60 sequences, 12 genetic clusters (I to XII) and an unstable sequence crowd (xiii) were identified. The robustness of the genetic clusters was confirmed by analyses of rpoB and hemB sequences and ampC PCR-RFLPs. Sequence crowd xiii split into two groups after rpoB analysis. Only three strains formed a cluster with the type strain of E. cloacae, indicating that the minority of isolates identified as E. cloacae truly belong to the species; 13% of strains grouped with other type strains of the genus, suggesting that the phenotypes of these species seem to be more heterogeneous than so far believed. Three clusters represented 70% of strains, but none of them included a type or reference strain. The genetic clustering presented in this study might serve as a framework for future studies dealing with taxonomic, evolutionary, epidemiological, or pathogenetic characteristics of bacteria belonging to the E. cloacae complex.

Chromosomal ampC genes in Enterobacter species other than Enterobacter cloacae, and ancestral association of the ACT-1 plasmid-encoded cephalosporinase to Enterobacter asburiae

The amplification and sequence of ampC genes in Enterobacter asburiae, Enterobacter cancerogenus, Enterobacter dissolvens, Enterobacter hormaechei and Enterobacter intermedius bring the number of known cephalosporinase sequences from the genus Enterobacter to seven. Expression in Escherichia coli of the ampC genes from E. asburiae, E. hormaechei and E. intermedius established the functional nature of these genes. ampC from E. asburiae shows 96.5% identity to bla(ACT-1) encoding a plasmid-borne cephalosporinase previously believed to derive from Enterobacter cloacae. The reassignment of ACT-1 ancestry to E. asburiae is confirmed by the 95.5% identity between ampR upstream of bla(ACT-1) and ampR from E. asburiae.